iiinova — where your digital self keeps evolving

Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 02/10/2026

I have migrated from @akademienl , which was a wonderful instance but unfortunately and understandably shutting down. I hope to share here on genomics.social some of the work I do with #uniprot #rhea and #swisslipids. Specifically around keeping that data #FAIR and useable. I am most vocal […]

genomic.social

Original post on genomic.social

BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 18/09/2026

Reposted by Jerven Bolleman

"Building InterMine databases from RDF Portal" doi.org/10.37044/osf.io/dqm3j_v1 #biohackathon #rdf #intermine #BH26JP "The public HumanMine has not had a data release since February 2022. RDF Portal, operated by the Database Division for Life […] [Original post on fediscience.org]

Figure 1:How a mine gets its data. (a) Today each HumanMine source has its own loader, written and maintained as code by the mine’s developers. (b) With RDF Portal and rdfc2im, the work for each dataset moves upstream: RDF Portal holds each dataset’s RDF and an rdf-config model written in rdf-config’s common form, made once and reused by every consumer. rdfc2im is one tool for all sources, and what remains for each source is a curated mapping, kept as data with the evidence for every row. Tags show scope (per source, per dataset, shared, reused), effort (manual, automatic) and form (code, template, data).

Marloes de Koning :check: @marloesdekoning.nrc.social.ap.brid.gy · 18/09/2026

Reposted by Jerven Bolleman

Deze video van de Noorse consumentenbond over #enshittification kennen jullie vast al, maar voor mij was hij nieuw en ik moet lachen. vimeo.com/1168468796 Digital products and services keep getting worse. In the new report Breaking Free: Pathways to a fair technological future, the […]

mastodon.nl

Original post on mastodon.nl

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Reposted by Jerven Bolleman

Kingsley Uyi Idehen @kidehen.mastodon.social.ap.brid.gy · 18/09/2026

RE: mastodon.social/@openlink/117288641… Open protocols beat proprietary plumbing. In the age of AI, that advantage compounds: LLMs are trained on those protocols, so the Agents they power become powerful generic clients you drive in natural language.

mastodon.social

jonny (nonvenomous) @jonny.neuromatch.social.ap.brid.gy · 08/09/2026

Reposted by Jerven Bolleman

OpenAI claims that they used 300 billion output tokens from a swarm of ~10,000 concurrent instances of an internal model that is almost certainly larger and more expensive to run than GPT-6. That's the total token output, including exploring related problems, which, along with spying on other […]

neuromatch.social

Original post on neuromatch.social

jonny (nonvenomous) @jonny.neuromatch.social.ap.brid.gy · 08/09/2026

Reposted by Jerven Bolleman

> The route to the Clay problem through a smooth force, options c and d in Fefferman’s statement of the problem, is the route Luis and Diego opened and the one Levent and I had quietly chosen to attack. Almost nobody else I know of was working on it. It is not the direction one arrives at in a […]

neuromatch.social

Original post on neuromatch.social

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Reposted by Jerven Bolleman

Charles Tapley Hoyt @cthoyt.scholar.social.ap.brid.gy · 04/09/2026

blogged today about ChEBI, data properties in OWL ontologies, computational chemistry, atomic numbers, and basis sets cthoyt.com/2026/09/04/chebi-atomic-… all part of @NFDI4Chem #obo #owl #chebi #obofoundry #nfdi #nfdi4chem

A diagram showing how ontology inference could be used to connect molecules and applicable basis sets for computational chemistry experiments

Bert Hubert NL 🇺🇦🇪🇺🇺🇦 @bert-hubert.mastodon.nl.ap.brid.gy · 01/09/2026

Reposted by Jerven Bolleman

RE: social.overheid.nl/@rivm/1171945711… Met dit vaccin zijn we hard op weg baarmoederhalskanker uit te roeien. Het is een wetenschappelijk hoogstandje en wordt aanbevolen voor jongens en meisjes. En het voorkomt ONVOOSTELBAAR VEEL LEED. Ik kan kippenvel krijgen van wat dit […]

mastodon.nl

Original post on mastodon.nl

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Anthony Horton @spacelizard.aus.social.ap.brid.gy · 01/09/2026

Microsoft: Use the web versions of our Office apps! They're great! Me: So how do I create a new document based on my employer's .dotx template? Microsoft: Oh, that's easy, you download it from SharePoint to your computer, use the desktop version of Word to create a new document from the […]

aus.social

Original post on aus.social

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Reposted by Jerven Bolleman

Dr. Serge Zaka @sergezaka.bsky.social · 31/08/2026

Si l’on compare 2026, 2022, 2003 et 1976 en termes d’intensité maximale de la sécheresse (c’est-à-dire le niveau minimal d’eau disponible pour les plantes atteint au cours de l’année) il n’y a pas photo : 2026 se démarque très largement des autres années (première carte). 9/10

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 31/08/2026

#eccb2016 @SIB member Anais Mottaz talking about "enabling federated genomic data discovery and analysis with GA4GH standards across ELIXIR".

Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 31/08/2026

#eccb2026 @elixir_europe talking about the needs for sustainable infrastructure. Welcome new arrivals Malta and Slovakia.

Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 31/08/2026

#eccb2026 Jeremy Farrar #WHO "Science in a Changing World". Looking back #eccb starting 25 years ago and how the field has changed as much. We need to think about our future and where will we be in 25 years. Some of the leaders of that future are in the room today.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 31/08/2026

#eccb opening performance was fantastic. Hope to share a video later. It was a great impression of the challenges we face, and how only together we can beat them. The visuals showed that connections are critical!

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 31/08/2026

#eccb has the privilege to listen to @GuyParmelin. Always very interesting to hear the political view on our work in general. I think it is important that we as scientists take into account that we are performing a social service and we should be careful in how we use societies resources.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 31/08/2026

#eccb Anne Hiltpold, Pressident of the State Council of the Republic and Canton #Geneva. Data was the oil of the 20th century, no longer true.We use #data on the fly. Raw data like #oil has no value by itself. We need to transform this respecting ethics and morals. Humanity faces challenges, all […]

Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 31/08/2026

#UniGe Prof Leuba recounts the start of #UniProt with #Swiss-Prot in 1986 (where I work). How this is an example of making data understandable, and how quality is a work in progress. This is a requirement for all scientific fields. This is not a technical question: but of scientific quality and […]

Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 31/08/2026

@dessimoz 30years ago #unige helped start @SIB at that time #bioinformatics was a fledgling field. The rector of #UniGe Prof. Leuba welcomes #eccb participants. Q? what makes data scientifically valuable? Generate and analyzing data is growing, but this depends on the quality of the data […]

Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 31/08/2026

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simonedemontmollin.ch describes how society #genevalovesdata needs the work by #scientists and how they need society. To make #democracy work we need reasoned voices. The people need to maintain control over data so that they can act in their rightful sovereign manner.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 31/08/2026

@dessimoz of @SIB opening the #eccb. 1st time in #Geneva a place for exchanging ideas and promoting collaboration.

Stephen Turner @stephenturner.us · 21/08/2026

Reposted by Jerven Bolleman

"We urge funders to treat biological databases as a shared infrastructure, as they do biobanks and particle accelerators. Without sustained investment, the life sciences risk building an ambitious future on a collapsing foundation."

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Reposted by Jerven Bolleman

George Macgregor @g3om4c.code4lib.social.ap.brid.gy · 11/08/2026

The #enshittification of the web arising from #AI is just so manifest. And I am so sick of it. Once again, our services are undergoing a protracted phase of #bot #swarming and -- despite best efforts -- knocking our services offline. In other words, the high value content that #LLMs rely on […]

code4lib.social

Original post on code4lib.social

grob (teeth era) 🇺🇦🏳️‍🌈🏳️‍⚧️ @grob.mstdn.social.ap.brid.gy · 10/08/2026

Reposted by Jerven Bolleman

@frameworkcomputer got owned. Or rather, their 3rd party business intelligence provider Metabase. So chances are, your name, address, phone number and email are now in the hands of criminals if you entrusted these to Framework. Source: I was informed by Framework to be among affected people […]

mstdn.social

Original post on mstdn.social

Harald Klinke @hxxxkxxx.det.social.ap.brid.gy · 10/08/2026

Reposted by Jerven Bolleman

The Rijksmuseum has moved from “an API” toward a machine-readable knowledge infrastructure: Objects, people, places and concepts receive persistent URIs, not just web addresses, but machine-readable identities that can be linked across systems. The shift is from “search a museum database” to an […]

det.social

Original post on det.social

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Reposted by Jerven Bolleman

Egon Willigh☮gen 🟥 @egonw.mastodon.social.ap.brid.gy · 13/07/2026

RE: mastodon.social/@the_fair_elephant/… "Germany agreed to continue the funding for National Research Data Infrastructure (NFDI) until 2038" That is awesome!

mastodon.social

Osma A 🇫🇮🇺🇦 @osma.fishpool.org · 10/07/2026

Reposted by Jerven Bolleman

Nordstream is a "mystery", in that the people who are most in the position to clear what happened, are the least interested in publicly discussing it. So convenient explanations get all the air time. @anderspuck asks some of the less convenient questions. muku.dk/w/rhFeixKjy3HyV98yBNegZE

muku.dk

Did a group of Ukrainians blow up Nord Stream?

A Ukrainian citizen has been charged in Germany over the Nord Stream sabotage, and a new book lays out how a group of Ukrainians allegedly did it. A lot of Western media now treats the case as solv...

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Reposted by Jerven Bolleman

Marc Robinson-Rechavi @marcrr.ecoevo.social.ap.brid.gy · 29/06/2026

Noticing that the public data reused in #SMBE2026 symposium Evolutionary Genomics from Public Repositories is always genomes / DNA rather than expression / transcriptomes. Hopefully in future years this will change thanks to work at @bgeedb and elsewhere!

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Reposted by Jerven Bolleman

Marc Robinson-Rechavi @marcrr.ecoevo.social.ap.brid.gy · 24/06/2026

RE: ecoevo.social/@marcrr/1163341022256… If you're going to #SMBE2026 @officialSMBE Copenhagen by train, share your plans and experience on #NoFlySMBE. Let's make #NoFlyAcademics normal and visible! I'm going Lausanne-Basel, night train 😴 Basel-Hamburg, and finally […]

ecoevo.social

Original post on ecoevo.social

Marc Robinson-Rechavi @marcrr.ecoevo.social.ap.brid.gy · 11/06/2026

Reposted by Jerven Bolleman

Melzer: Why are there few plant species, and why so many flowering plants? In ferns or gymnosperms, reproductive and vegetative stages are not strongly separated, e.g. vegetative stage growing from a pine cone on the tree. #EED2026

Laurens Hof @mastodon.laurenshof.online · 09/06/2026

Reposted by Jerven Bolleman

the cyberpunk present is weird as fuck: the latest Shai Hulud malware wave contains an LLM prompt to create biological weapons and nuclear weapons, with the purpose to trip LLM safety refusals so that LLM-based code scanning wont see the malware […] [Original post on indieweb.social]

llm prompt for creating bioweapons and nuclear weapons

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 27/05/2026

Google-deepmind wrote some skills for using #UniProt and I really second the advice "If a complex search query fails, try to use SPARQL instead of giving up."

Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 19/05/2026

RE: hachyderm.io/@Elendol/1166009574904… Yeah, I love them for it! It is so cool that one can connect data from grants with data about grants :D

hachyderm.io

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developer.overheid.nl @developer.social.overheid.nl.ap.brid.gy · 19/05/2026

🥳 Goed nieuws voor iedereen wel eens een kaartviewer moet bouwen: het Kadaster heeft nu een open source project dat precies dit voor je doet! 🔩 De viewer is makkelijk te configureren en je kan hem naar eigen smaak stylen. Meer hierover lees je op […]

social.overheid.nl

Original post on social.overheid.nl

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Reposted by Jerven Bolleman

jonny (nonvenomous) @jonny.neuromatch.social.ap.brid.gy · 05/05/2026

RE: mathstodon.xyz/@albertcardona/11652… The fact that FlyBase has trouble getting funding should be a blaring red siren that our funding mechanisms don't even come close to valuing the infrastructure that's critical to science. There's a big banner on the homepage that […]

neuromatch.social

Original post on neuromatch.social

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Reposted by Jerven Bolleman

École des Bro-Arts @aphyr.woof.group.ap.brid.gy · 01/05/2026

I dunno if this is typical or not but writing a conference talk is about a solid week of work for me. I started this 35 minute talk on Sunday. It took three days to write and illustrate the slides, figuring out what I wanted to say, the right metaphors, sequencing, callbacks, and visuals. Then […]

woof.group

Original post on woof.group

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Reposted by Jerven Bolleman

WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 03/04/2026

@Marvin upgraded our SPARQL interface. It now show a title and a description, and making it easier to navigate the example queries: sparql.wikipathways.org (maybe do a hard reload) #openscience #bioinformatics

Screenshot of the linked SPARQL endpoint interface. It shows three main panels below a title bar (which includes the endpoint URL). One panel shows the title, description, and SPARQL query currently being "edited". The right-hand side panel shows a list of queries, now with easier to read query names. The bottom panel is still the results table. The query used is the one listing all authors, sorted descending by the number of pathways they initiated. For each author, the number of pathways, their name, ORCID, and WikiPathways account page is listed.

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 24/03/2026

#SWAT4HCLS nice to see #qlever with a 1 trillion triple dataset. Or four UniProts ;)

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Jerven Bolleman @jervenbolleman.genomic.social.ap.brid.gy · 24/03/2026

Always a pleasure to see my friends from #SPHN present their successes and improvements in #securely providing clinical data to research for next gen medicine and care! […]